I'd definitely agree here. In general, stuff where multiple processes need to talk to each other but are in separate containers is frustrating. So modding tools stumble a bit. Also, things that require login via a browser, which then redirects back to the application (for example, Unity opens a login page then goes back) - when it's running through Proton or in a container, it'll open in the browser on the host system, which then can't get back to it.

That may just be a me being stupid issue, but it's annoying.

Still keep using it because it's great, and no ads or crap is lovely.